Can you describe more what you are looking for? Maybe provide a screenshot of exactly the colors. I can imagine our providing the colors for the multi-peptide graphs as a peptide property in either RGB or Hex format. You can get and even set these colors for transitions and precursors under Tools > Options - Display - Color Scheme, where you can choose from several available schemes or create your own, or use <Edit current...> to get the RGB and Hex values for the current color scheme.
Hope this helps. But, do provide a bit more information on what you are looking for.